DEV-2648: Merge kepler to master #1104
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… counts (#819) * checkpoint * Add genomicFilter to cohort Filters in CanncerDistributionTable. * Update cancerDistributionTableColumns memo dependencies --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
* Update unit test Remove setid from create set, remove partial for gene table toggle * investigate set creation * revert caseset creation changes --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
…Case Page SMTable (#818) * fix filter plus implement 2 downloads * remove unnecessary var --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* fix(PEAR-1264): adjust font size, gap & add no prewrap * fix(PEAR-1264): update unit test * fix(PEAR-1264): pr feedback * fix(PEAR-1264): minor styling changes * fix(PEAR-1264): - gap between btns
Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* Use the LoadingOverlay component to mask the OncoMatrix and Gene Expression plots while data is being loaded and processed * prototype the BAM download app; update the pp client version to 2.31.1 * fix the SequenceReadWrapper types and tests
* fixed the issue and added tests * change solution after comments * move to else --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* fix a few accessibility issues * remove image of from the alt text --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
* PEAR-1441: add tooltip to table search with unique styling * PEAR-1522: upgrade @types/react and @types/react-dom to 18 * Revert "PEAR-1522: upgrade @types/react and @types/react-dom to 18" This reverts commit 0584543. * PEAR-1522: use mantine tooltip * PEAR-1522: clean up styling * PEAR-1441: add code to properly set z-index of modals * PEAR-1441: fix font size and font * PEAR-1441: Component name should be PascalCased --------- Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>
* PEAR-1645: prepare 2.11.0 release (#825) * PEAR-1645 fix typo * PEAR-1645 introduce typo * PEAR-1645 remove typo * PEAR-1655: gdcapi int test, change start from 0 to 1 (#832) * PEAR-1387: Fix Cannot create cohort when 1 case selected (#796) * fixed the issue and added tests * change solution after comments * move to else --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local> * PEAR-1627: Fix 508 Compliance - GDC Portal v2 home page - (#827) * fix a few accessibility issues * remove image of from the alt text --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local> * PEAR-1652: change summary chart to use explore (#826) Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> * PEAR-1441: add tooltip to table search with unique styling (#778) * PEAR-1441: add tooltip to table search with unique styling * PEAR-1522: upgrade @types/react and @types/react-dom to 18 * Revert "PEAR-1522: upgrade @types/react and @types/react-dom to 18" This reverts commit 0584543. * PEAR-1522: use mantine tooltip * PEAR-1522: clean up styling * PEAR-1441: add code to properly set z-index of modals * PEAR-1441: fix font size and font * PEAR-1441: Component name should be PascalCased --------- Co-authored-by: ocshawn <shawnoconnor@uchicago.edu> * change start from 0 to 1 --------- Co-authored-by: Paribartan Dhakal <101295912+paribartandhakal@users.noreply.github.com> Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local> Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com> Co-authored-by: ocshawn <shawnoconnor@uchicago.edu> * PEAR-1642: fix error from opening set operations from cohort comparison, have error boundary kick the user to the homepage after they've encountered the error once (#828) * PEAR 1322 / 1621: Mutations button, survival plot in Mutations tab not plotting for a mutation (#691) * fix(PEAR-1322): update survival plot when mtn count btn is clicked * fix(PEAR-1322): plot top-most mutation after mtn button clicked in genes table * feat(PEAR-1322): plot topmost ssm on mutation count click only * fix(PEAR-1322): include symbol in legend label * fix(PEAR-1322): minor type change * fix(PEAR-1322): add expected error type * refactor(PEAR-1322): try to fix pipeline test * refactor(PEAR-1322): resolve build error * fix(PEAR-1322): add case filter * fix(PEAR-1322): pr feedback * fix(PEAR-1322): plot correct ssm after clicking mtn btn + clearing search * fix(PEAR-1322): pr feedback edge case * fix(PEAR-1322): plot topmost when unselecting and after clicking mtn btn * fix(PEAR-1322): remove log/comments * fix(PEAR-1322): missing deps lint warnings * fix(PEAR-1322): use useDeepCompare * remove uneeded dependency for SMTableContainer/useDeepCompareCallback * fix(PEAR-1322): revert some changes + feedback * fix(PEAR-1322): eslint deps lint * fix(PEAR-1322): revert * add TODO with reference to PEAR-1657 --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> --------- Co-authored-by: Jiakung Feng <69171880+jiakf@users.noreply.github.com> Co-authored-by: Jason Stiles <99777116+stilesj-uchicago@users.noreply.github.com> Co-authored-by: Paribartan Dhakal <101295912+paribartandhakal@users.noreply.github.com> Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local> Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu> Co-authored-by: Shawn O'Connor <ocshawn@ocshawn.com> Co-authored-by: ocshawn <shawnoconnor@uchicago.edu> Co-authored-by: Amy Lehman <amlehman77@gmail.com> Co-authored-by: Ali Lahrime <90918464+alilahrime@users.noreply.github.com>
* PEAR-1637 - labels for box plot, qq plot, and search input * PEAR-1637 - remove complementary role
Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* Remove noise from reducer warning, unmocked queries and svgr mock * Use mockReturnValue instead of mockImplmentation
…829) * fix accessibility issues * remove alt text --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* initial outline * add docs to eslint ignore * Add apendix * change typedoc output path * more sections and add figures * add case and file hooks section * Start create cohort section * Finish create cohort section * add alter cohort and counts * add chart examples * add Chart Section * start component section: * complete the Component section * start tutorial section * Finish first draft * Add Application figure * clean up grammar * fix component image size complete table of contents * add md-to-pdf and remove space from dev guide filename * fix heading level * fix caption location * fix whitespace issue * whitespace..again * Update Developers_Guide.md * change title * Update Developers_Guide.md * update version of puppeteer * remove md-to-pdf --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
…ohort (#840) * add validation for disallowing naming cohort as unsaved_cohort * fix unit tests * make style changes * fix unit tests * update test description --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
…styling, and small code cleanup (#852) Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>
Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* PEAR-1564 - implement save as feature * PEAR-1564 - add condition to test * PEAR-1564 - correct data-testid for dropdown * PEAR-1564 - PR feedback, remove margin on button, discard changes correctly, make new cohort the current cohort
* PEAR-1575 adds support for new portal V2 banner component; remove support for V1 component * PEAR-1575 updates tests
…o guides (#854) * add a send feedback modal and new nav for video guides * add aria label to copy icon * add a period * a few padding fixes --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* Begin fixing failures due to cohort create changes QA-2105 * Continue fixing failures due to cohort create changes QA-2105 * Made header waits uniform QA-2105 * Updated discard changes test for cohort create changes QA-2105 * Added comment for before suite function QA-2105 * Put back original navigation, added additional waits QA-2105 --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
* Added IDs to project summary modal QA-2177 * Added IDs to case summary modal QA-2177 * Added IDs to file summary modal QA-2177 * Added IDs to gene summary modal QA-2177 * Added IDs to mutation summary modal QA-2177 * Added IDs to annotation summary modal QA-2177
…#1036) * remove caseSet creation to test dynamic cohorts * change GeneTable query to case_filters * update GraphQL for Gene Summary tables * update cnvTotals/ssmsTotals for Gene Summary * update SSMSTable query to account for case_filters * fix issue with getSSMGeneTestedCases * change geneParam back to optional for getSSMGeneTestedCases * change Gene cohort creation to dynamic_cohorts * update merge function * remove attempt to merge filterset to create dynamic oohort from genomic apps and tables. * change initial filters for GeneTable * fix wrong count in Mutation table * still survival plot * test of survival again * fix Genes Table * clean up code * minor formatting change * correct call to survivalApiSlice * correct issue with SSMSTable * change cnvPlot to use case_filters * why won't rows open? * fix lint issues * fix PEAR-1043 * remove console.log * remove case set creation for genes/ssms * update tests * join comentted code * update comments * swap use of selector for currentCohortGeneAndSSMS for currentCohortFilters * remove filters from Cohort:caseSets * update unit test * remove old code for case_sets * remove depreciated code * import CoreState in facets/hooks * remove mergeFilterSet * fix PEAR-1459 * remove typo --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
… strands the tooltip and removes the focus (#1054)
* update the proteinpaint-client version to 2.50.0; handle empty userDetails.data in sequence read app * replace useEffect with useDeepCompareEffect in ProteinPaint-based tools
…ownload + no loading spinners (#1047) * adding loading indicator + download controlled files > case summary * reset the state of the modal * add logic for resetting --------- Co-authored-by: HEAL-2 <heal-2@HEAL-2s-MacBook-Pro.local>
Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>
* PEAR-1851 - add set_type and intent as required fields when creating a set * PEAR-1851 - change instances where we are creating a set to use in a cohort to portal * PEAR-1851 - missed a portal update in cancer distribution table * add intent, set_type to SelectCohortsModal * change STJUDE set creation to portal * update setop's cohort creation * update setop's cohort creation --------- Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
STJUDE: update the proteinpaint-client version to 2.52.0 (#1068)
Also added a npm script to make this easier in the future.
* PEAR-1878: fix cDAVE toggle tooltips * PEAR-1878: update tooltip to only point at name --------- Co-authored-by: ocshawn <shawnoconnor@uchicago.edu>
* standardize title in the vertical table * missing bold in primary site and project --------- Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
* PEAR-1843 - configure datadog view names, add version, only init datadog on prod build * PEAR-1843 - switch to use NEXT_PUBLIC var, update annotation browsert name
Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
Co-authored-by: craigrbarnes <craigrbarnes@uchicago.edu>
Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
…ge loads (#1089) * QA-1949: Automated test for cohort comparison download TSV (#1074) * Automated test for cohort comparison download TSV QA-1949 * Added tag to spec file QA-1949 * QA-2178: update test automation 2.13.0 (#1071) * Updates to test automation for kepler release QA-2178 * Added smoke test, removed print line QA-2178 * PEAR-1835: Responsive homepage header (#1057) * initial setup * more updates * added a drawer for nav bar in smaller screens * consolidating logic/components for links * confirm style matches * icon styles * made styling changes - gdc apps, drawer comp * fix accessibility issues * fix z-index * fix failing tests + accessibility * aria-hidden to a few icons * code cleanup --------- Co-authored-by: HEAL-2 <heal-2@HEAL-2s-MacBook-Pro.local> Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local> * PEAR-1839: Add annotations table to case summary page, adjust links (#1078) * PEAR-1839 - add annotation table to case summary * PEAR-1839 - Add annotations table to case summary * PEAR-1839 - jk, this change was not correct * PEAR-1839 - fix annotation link conditional * PEAR-1839 - remove table title * PEAR-1898 - scroll to file section on load in case view * PEAR-1898 - eslint warning --------- Co-authored-by: bpierce01 <103586536+bpierce01@users.noreply.github.com> Co-authored-by: craigrbarnes <craig.barnes@intelligentlight.com> Co-authored-by: Paribartan Dhakal <101295912+paribartandhakal@users.noreply.github.com> Co-authored-by: HEAL-2 <heal-2@HEAL-2s-MacBook-Pro.local> Co-authored-by: Paribartan Dhakal <paribartandhakal@Paribartans-CTDS-MacBook-Pro.local>
craigrbarnes
requested changes
May 3, 2024
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Description
Merge kepler release (2.13.0) into master
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